Inhibitors with induced fit, will show significant conformational change from the apo form. Just removing the inhibitor from a holo form will keep it in a conformation that may not be physiologically relevant for an apo form. I would suggest you to start from an apo form since that is avilable.

Given that you have the apo structure available, you can determine how justifiable your choice is by overlaying the structures and calculating RMSD, looking at alignment of critical residues, etc. Given that beta-secretase as an important active-site loop whose dynamics are important, this can be a big difference. If your MD simulation(s) from the apo form you create resemble the actual apo state, then what you did was probably justifiable. Simulating from both starting apo states would also be a logical approach and probably give you better sampling.

Dear Ismail,

In order to answer your question we should define the terms:

Apoenzyme- An enzyme that requires a cofactor but does not have one bound. An apoenzyme is an inactive enzyme, activation of the enzyme occurs upon binding of an organic or inorganic cofactor.

Holoenzyme- An apoenzyme together with its cofactor. A holoenzyme is complete and catalytically active. Most cofactors are not covalently bound but instead are tightly bound. However, organic prosthetic groups such as an iron ion or a vitamin can be covalently bound.

The active site of the holoenzyme is some what is distorted due to the presence of the coenzyme  (covalently or tightly bound) and inhibitor. Therefore, using the holoenzyme and removing the inhibitor conenzyme from its active site to generate an apoenzyme will lead to inaccurate simulation results.

Only in cases in which the coenzyme and inhibitores do not affect the shape of the enzyme's active site, calculations on the entity generated after removing the coenzyme and inhibitor will be acceptable and quite accurate.

I recommend that you run your calculations on apoenzymes having known crystal structure. 

Please note that the consensus among all biochemists is that the enzyme active site is changing upon binding to substrates or inhibitors.

Hoping this will be helpful,

Rafik

Dear Ismail,

In order to answer your question we should define the terms:

Apoenzyme- An enzyme that requires a cofactor but does not have one bound. An apoenzyme is an inactive enzyme, activation of the enzyme occurs upon binding of an organic or inorganic cofactor.

Holoenzyme- An apoenzyme together with its cofactor. A holoenzyme is complete and catalytically active. Most cofactors are not covalently bound but instead are tightly bound. However, organic prosthetic groups such as an iron ion or a vitamin can be covalently bound.

The active site of the holoenzyme is some what is distorted due to the presence of the coenzyme  (covalently or tightly bound) and inhibitor. Therefore, using the holoenzyme and removing the inhibitor conenzyme from its active site to generate an apoenzyme will lead to inaccurate simulation results.

Only in cases in which the coenzyme and inhibitores do not affect the shape of the enzyme's active site, calculations on the entity generated after removing the coenzyme and inhibitor will be acceptable and quite accurate.

I recommend that you run your calculations on apoenzymes having known crystal structure. 

Please note that the consensus among all biochemists is that the enzyme active site is changing upon binding to substrates or inhibitors.

Hoping this will be helpful,

Rafik

Thank you all.